The goal is to throw the red, yellow, green and blue eggs into the Piranha Plant of the same color to earn points. If the wrong egg is thrown into a wrong colored Piranha Plant (e.g. Red Egg into Blue Piranha Plant), the Piranha Plant will proceed to spit a Fireball at the player who gave them the wrong egg, forcing them to duck. Occasionally, the players may find a Bomb amongst the eggs. If thrown at a Piranha Plant, the player will get three points. If thrown at a rival player (forcing them to duck for cover, as with fireballs), they will lose some points. Also, every now and then a giant Purple Piranha Plant will replace the other three for a few seconds; it will be able to eat all kinds of eggs, but will spit Fireballs at all players. The player with the most points at the end of the sixty-second time limit (90 in Special Mode), wins the game.

Piranha Panic is also featured in Challenge Mode, where the player is able to challenge three Shy Guys to a game of Piranha Panic. In Mario Super Sluggers, the rules change. Players must prevent their Piranha Plants from reaching them by throwing balls at the plant. Every hit will fill up the player's gauge. Once the gauge reaches its maximum, the player can throw a bomb.